Job ID = 10165981 SRX = SRX8331155 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... fastq に変換しました。 bowtie でマッピング中... Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:12:58 36309791 reads; of these: 36309791 (100.00%) were unpaired; of these: 431759 (1.19%) aligned 0 times 30634843 (84.37%) aligned exactly 1 time 5243189 (14.44%) aligned >1 times 98.81% overall alignment rate Time searching: 00:12:58 Overall time: 00:12:58 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 7 sequences. [bam_sort_core] merging from 16 files... [bam_rmdupse_core] 16199956 / 35878032 = 0.4515 in library ' ' BAM に変換しました。 Bed ファイルを作成中... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Thu, 08 Oct 2020 20:42:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX8331155/SRX8331155.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX8331155/SRX8331155.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX8331155/SRX8331155.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX8331155/SRX8331155.bam'] # control file = None # effective genome size = 9.00e+07 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-05 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Thu, 08 Oct 2020 20:42:01: #1 read tag files... INFO @ Thu, 08 Oct 2020 20:42:01: #1 read treatment tags... INFO @ Thu, 08 Oct 2020 20:42:07: 1000000 INFO @ Thu, 08 Oct 2020 20:42:12: 2000000 INFO @ Thu, 08 Oct 2020 20:42:17: 3000000 INFO @ Thu, 08 Oct 2020 20:42:23: 4000000 INFO @ Thu, 08 Oct 2020 20:42:28: 5000000 WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Thu, 08 Oct 2020 20:42:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX8331155/SRX8331155.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX8331155/SRX8331155.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX8331155/SRX8331155.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX8331155/SRX8331155.bam'] # control file = None # effective genome size = 9.00e+07 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-10 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Thu, 08 Oct 2020 20:42:31: #1 read tag files... INFO @ Thu, 08 Oct 2020 20:42:31: #1 read treatment tags... INFO @ Thu, 08 Oct 2020 20:42:34: 6000000 INFO @ Thu, 08 Oct 2020 20:42:39: 1000000 INFO @ Thu, 08 Oct 2020 20:42:40: 7000000 INFO @ Thu, 08 Oct 2020 20:42:46: 2000000 INFO @ Thu, 08 Oct 2020 20:42:46: 8000000 INFO @ Thu, 08 Oct 2020 20:42:52: 9000000 INFO @ Thu, 08 Oct 2020 20:42:52: 3000000 INFO @ Thu, 08 Oct 2020 20:42:57: 10000000 INFO @ Thu, 08 Oct 2020 20:42:59: 4000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Thu, 08 Oct 2020 20:43:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX8331155/SRX8331155.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX8331155/SRX8331155.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX8331155/SRX8331155.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX8331155/SRX8331155.bam'] # control file = None # effective genome size = 9.00e+07 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-20 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Thu, 08 Oct 2020 20:43:01: #1 read tag files... INFO @ Thu, 08 Oct 2020 20:43:01: #1 read treatment tags... INFO @ Thu, 08 Oct 2020 20:43:03: 11000000 INFO @ Thu, 08 Oct 2020 20:43:06: 5000000 INFO @ Thu, 08 Oct 2020 20:43:09: 1000000 INFO @ Thu, 08 Oct 2020 20:43:09: 12000000 INFO @ Thu, 08 Oct 2020 20:43:13: 6000000 INFO @ Thu, 08 Oct 2020 20:43:15: 13000000 INFO @ Thu, 08 Oct 2020 20:43:16: 2000000 INFO @ Thu, 08 Oct 2020 20:43:20: 7000000 INFO @ Thu, 08 Oct 2020 20:43:21: 14000000 INFO @ Thu, 08 Oct 2020 20:43:24: 3000000 INFO @ Thu, 08 Oct 2020 20:43:27: 8000000 INFO @ Thu, 08 Oct 2020 20:43:27: 15000000 INFO @ Thu, 08 Oct 2020 20:43:31: 4000000 INFO @ Thu, 08 Oct 2020 20:43:33: 16000000 INFO @ Thu, 08 Oct 2020 20:43:34: 9000000 INFO @ Thu, 08 Oct 2020 20:43:38: 17000000 INFO @ Thu, 08 Oct 2020 20:43:39: 5000000 INFO @ Thu, 08 Oct 2020 20:43:40: 10000000 INFO @ Thu, 08 Oct 2020 20:43:44: 18000000 INFO @ Thu, 08 Oct 2020 20:43:46: 6000000 INFO @ Thu, 08 Oct 2020 20:43:47: 11000000 INFO @ Thu, 08 Oct 2020 20:43:50: 19000000 INFO @ Thu, 08 Oct 2020 20:43:53: 7000000 INFO @ Thu, 08 Oct 2020 20:43:54: #1 tag size is determined as 55 bps INFO @ Thu, 08 Oct 2020 20:43:54: #1 tag size = 55 INFO @ Thu, 08 Oct 2020 20:43:54: #1 total tags in treatment: 19678076 INFO @ Thu, 08 Oct 2020 20:43:54: #1 user defined the maximum tags... INFO @ Thu, 08 Oct 2020 20:43:54: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 08 Oct 2020 20:43:54: 12000000 INFO @ Thu, 08 Oct 2020 20:43:54: #1 tags after filtering in treatment: 19678076 INFO @ Thu, 08 Oct 2020 20:43:54: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 08 Oct 2020 20:43:54: #1 finished! INFO @ Thu, 08 Oct 2020 20:43:54: #2 Build Peak Model... INFO @ Thu, 08 Oct 2020 20:43:54: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 08 Oct 2020 20:43:56: #2 number of paired peaks: 185 WARNING @ Thu, 08 Oct 2020 20:43:56: Fewer paired peaks (185) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 185 pairs to build model! INFO @ Thu, 08 Oct 2020 20:43:56: start model_add_line... INFO @ Thu, 08 Oct 2020 20:43:56: start X-correlation... INFO @ Thu, 08 Oct 2020 20:43:56: end of X-cor INFO @ Thu, 08 Oct 2020 20:43:56: #2 finished! INFO @ Thu, 08 Oct 2020 20:43:56: #2 predicted fragment length is 1 bps INFO @ Thu, 08 Oct 2020 20:43:56: #2 alternative fragment length(s) may be 1,28,49,52,566 bps INFO @ Thu, 08 Oct 2020 20:43:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX8331155/SRX8331155.05_model.r WARNING @ Thu, 08 Oct 2020 20:43:56: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 08 Oct 2020 20:43:56: #2 You may need to consider one of the other alternative d(s): 1,28,49,52,566 WARNING @ Thu, 08 Oct 2020 20:43:56: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 08 Oct 2020 20:43:56: #3 Call peaks... INFO @ Thu, 08 Oct 2020 20:43:56: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 08 Oct 2020 20:44:01: 8000000 INFO @ Thu, 08 Oct 2020 20:44:01: 13000000 INFO @ Thu, 08 Oct 2020 20:44:08: 14000000 INFO @ Thu, 08 Oct 2020 20:44:08: 9000000 INFO @ Thu, 08 Oct 2020 20:44:14: 15000000 INFO @ Thu, 08 Oct 2020 20:44:15: 10000000 INFO @ Thu, 08 Oct 2020 20:44:21: 16000000 INFO @ Thu, 08 Oct 2020 20:44:23: 11000000 INFO @ Thu, 08 Oct 2020 20:44:24: #3 Call peaks for each chromosome... INFO @ Thu, 08 Oct 2020 20:44:27: 17000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Thu, 08 Oct 2020 20:44:30: 12000000 INFO @ Thu, 08 Oct 2020 20:44:34: 18000000 INFO @ Thu, 08 Oct 2020 20:44:37: 13000000 INFO @ Thu, 08 Oct 2020 20:44:38: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX8331155/SRX8331155.05_peaks.xls INFO @ Thu, 08 Oct 2020 20:44:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX8331155/SRX8331155.05_peaks.narrowPeak INFO @ Thu, 08 Oct 2020 20:44:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX8331155/SRX8331155.05_summits.bed INFO @ Thu, 08 Oct 2020 20:44:38: Done! pass1 - making usageList (0 chroms): 0 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Thu, 08 Oct 2020 20:44:40: 19000000 INFO @ Thu, 08 Oct 2020 20:44:45: 14000000 INFO @ Thu, 08 Oct 2020 20:44:45: #1 tag size is determined as 55 bps INFO @ Thu, 08 Oct 2020 20:44:45: #1 tag size = 55 INFO @ Thu, 08 Oct 2020 20:44:45: #1 total tags in treatment: 19678076 INFO @ Thu, 08 Oct 2020 20:44:45: #1 user defined the maximum tags... INFO @ Thu, 08 Oct 2020 20:44:45: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 08 Oct 2020 20:44:45: #1 tags after filtering in treatment: 19678076 INFO @ Thu, 08 Oct 2020 20:44:45: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 08 Oct 2020 20:44:45: #1 finished! INFO @ Thu, 08 Oct 2020 20:44:45: #2 Build Peak Model... INFO @ Thu, 08 Oct 2020 20:44:45: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 08 Oct 2020 20:44:46: #2 number of paired peaks: 185 WARNING @ Thu, 08 Oct 2020 20:44:46: Fewer paired peaks (185) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 185 pairs to build model! INFO @ Thu, 08 Oct 2020 20:44:46: start model_add_line... INFO @ Thu, 08 Oct 2020 20:44:47: start X-correlation... INFO @ Thu, 08 Oct 2020 20:44:47: end of X-cor INFO @ Thu, 08 Oct 2020 20:44:47: #2 finished! INFO @ Thu, 08 Oct 2020 20:44:47: #2 predicted fragment length is 1 bps INFO @ Thu, 08 Oct 2020 20:44:47: #2 alternative fragment length(s) may be 1,28,49,52,566 bps INFO @ Thu, 08 Oct 2020 20:44:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX8331155/SRX8331155.10_model.r WARNING @ Thu, 08 Oct 2020 20:44:47: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 08 Oct 2020 20:44:47: #2 You may need to consider one of the other alternative d(s): 1,28,49,52,566 WARNING @ Thu, 08 Oct 2020 20:44:47: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 08 Oct 2020 20:44:47: #3 Call peaks... INFO @ Thu, 08 Oct 2020 20:44:47: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 08 Oct 2020 20:44:51: 15000000 INFO @ Thu, 08 Oct 2020 20:44:58: 16000000 INFO @ Thu, 08 Oct 2020 20:45:05: 17000000 BigWig に変換しました。 INFO @ Thu, 08 Oct 2020 20:45:12: 18000000 INFO @ Thu, 08 Oct 2020 20:45:16: #3 Call peaks for each chromosome... INFO @ Thu, 08 Oct 2020 20:45:18: 19000000 INFO @ Thu, 08 Oct 2020 20:45:23: #1 tag size is determined as 55 bps INFO @ Thu, 08 Oct 2020 20:45:23: #1 tag size = 55 INFO @ Thu, 08 Oct 2020 20:45:23: #1 total tags in treatment: 19678076 INFO @ Thu, 08 Oct 2020 20:45:23: #1 user defined the maximum tags... INFO @ Thu, 08 Oct 2020 20:45:23: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 08 Oct 2020 20:45:23: #1 tags after filtering in treatment: 19678076 INFO @ Thu, 08 Oct 2020 20:45:23: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 08 Oct 2020 20:45:23: #1 finished! INFO @ Thu, 08 Oct 2020 20:45:23: #2 Build Peak Model... INFO @ Thu, 08 Oct 2020 20:45:23: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 08 Oct 2020 20:45:24: #2 number of paired peaks: 185 WARNING @ Thu, 08 Oct 2020 20:45:24: Fewer paired peaks (185) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 185 pairs to build model! INFO @ Thu, 08 Oct 2020 20:45:24: start model_add_line... INFO @ Thu, 08 Oct 2020 20:45:25: start X-correlation... INFO @ Thu, 08 Oct 2020 20:45:25: end of X-cor INFO @ Thu, 08 Oct 2020 20:45:25: #2 finished! INFO @ Thu, 08 Oct 2020 20:45:25: #2 predicted fragment length is 1 bps INFO @ Thu, 08 Oct 2020 20:45:25: #2 alternative fragment length(s) may be 1,28,49,52,566 bps INFO @ Thu, 08 Oct 2020 20:45:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX8331155/SRX8331155.20_model.r WARNING @ Thu, 08 Oct 2020 20:45:25: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 08 Oct 2020 20:45:25: #2 You may need to consider one of the other alternative d(s): 1,28,49,52,566 WARNING @ Thu, 08 Oct 2020 20:45:25: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 08 Oct 2020 20:45:25: #3 Call peaks... INFO @ Thu, 08 Oct 2020 20:45:25: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 08 Oct 2020 20:45:30: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX8331155/SRX8331155.10_peaks.xls INFO @ Thu, 08 Oct 2020 20:45:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX8331155/SRX8331155.10_peaks.narrowPeak INFO @ Thu, 08 Oct 2020 20:45:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX8331155/SRX8331155.10_summits.bed INFO @ Thu, 08 Oct 2020 20:45:30: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Thu, 08 Oct 2020 20:45:55: #3 Call peaks for each chromosome... INFO @ Thu, 08 Oct 2020 20:46:08: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX8331155/SRX8331155.20_peaks.xls INFO @ Thu, 08 Oct 2020 20:46:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX8331155/SRX8331155.20_peaks.narrowPeak INFO @ Thu, 08 Oct 2020 20:46:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX8331155/SRX8331155.20_summits.bed INFO @ Thu, 08 Oct 2020 20:46:08: Done! pass1 - making usageList (0 chroms): 0 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling